Adding WP Native Audio,Video Support (1 post)

I have created a WP Theme which plays self hosted audio and video using the shortcodes as below:

[audio]http://mydowmain.com/uploads/2013/01/myfile.mp3[/audio]
and for video
[video]http://mydowmain.com/uploads/2013/01/myfile.mp4[/video]

It uses HTML5 with a flash fallback and works perfectly.
The Issue I am facing is that most of the WP users do not know where to get the file link from.
Since WordPress has this functionality to upload videos & audios and the media can successfully recognize audio and video. I want to use my shortcode when someone selects an audio/video from media and clicks "Insert" in post.
How can I connect WP Native insert with my shortcode?
Any help would be appreciated.